Dear all
Is there any option or keyword to calculate the number of
hydrogen bonds in a solution. e.g., water?
I could not find such thing.
Bests
Mike
Sent with Mailtrack
Dear all
Is there any option or keyword to calculate the number of
hydrogen bonds in a solution. e.g., water?I could not find such thing.
not directly. if you only are interested in the total number of hydrogen
bonds, you could try to (ab-)use the dreiding hydrogen bond add-on
potential. http://lammps.sandia.gov/doc/pair_hbond_dreiding.html
if you add this as an interactions via pair style hybrid/overlay but with
the interaction energy set to zero (read the documentation very, very
carefully and compare results). please note, that there are different ways
to determine the hydrogen bond geometry and this pair style does not use
the most common one.
if you need something more specific, it is usually better to do this in
post-processing. e.g. VMD has a tool for that.
or you would have to write a custom compute style (e.g. based off of
compute cna/atom or coord/atom).
axel.